WO2009012418A3 - Method for generating aptamers with improved off-rates - Google Patents

Method for generating aptamers with improved off-rates Download PDF

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Publication number
WO2009012418A3
WO2009012418A3 PCT/US2008/070383 US2008070383W WO2009012418A3 WO 2009012418 A3 WO2009012418 A3 WO 2009012418A3 US 2008070383 W US2008070383 W US 2008070383W WO 2009012418 A3 WO2009012418 A3 WO 2009012418A3
Authority
WO
WIPO (PCT)
Prior art keywords
methods
aptamers
improved
producing
disclosure describes
Prior art date
Application number
PCT/US2008/070383
Other languages
French (fr)
Other versions
WO2009012418A2 (en
Inventor
Dominic Zichi
Sheri K Wilcox
Chris Bock
Daniel J Schneider
Bruce Eaton
Larry Gold
Original Assignee
Somalogic Inc
Dominic Zichi
Sheri K Wilcox
Chris Bock
Daniel J Schneider
Bruce Eaton
Larry Gold
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=40260081&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2009012418(A3) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority to DK08782010.6T priority Critical patent/DK2069529T3/en
Priority to JP2010517170A priority patent/JP5684568B2/en
Priority to EP08782010A priority patent/EP2069529B1/en
Priority to EP17181688.7A priority patent/EP3284832B1/en
Priority to MX2010000578A priority patent/MX2010000578A/en
Priority to EP09012809.1A priority patent/EP2172566B2/en
Priority to CN200880107336.0A priority patent/CN101809167B/en
Application filed by Somalogic Inc, Dominic Zichi, Sheri K Wilcox, Chris Bock, Daniel J Schneider, Bruce Eaton, Larry Gold filed Critical Somalogic Inc
Priority to AU2008275915A priority patent/AU2008275915B2/en
Priority to CA2696431A priority patent/CA2696431C/en
Priority to EP22162947.0A priority patent/EP4056711A1/en
Priority to MX2014005658A priority patent/MX344253B/en
Publication of WO2009012418A2 publication Critical patent/WO2009012418A2/en
Publication of WO2009012418A3 publication Critical patent/WO2009012418A3/en
Priority to HK09111389.7A priority patent/HK1133046A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1048—SELEX
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/115—Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/16—Aptamers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/33—Chemical structure of the base
    • C12N2310/334—Modified C
    • C12N2310/3341—5-Methylcytosine
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/10—Applications; Uses in screening processes
    • C12N2320/13—Applications; Uses in screening processes in a process of directed evolution, e.g. SELEX, acquiring a new function
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/205—Aptamer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2541/00—Reactions characterised by directed evolution
    • C12Q2541/10—Reactions characterised by directed evolution the purpose being the selection or design of target specific nucleic acid binding sequences
    • C12Q2541/101—Selex

Abstract

The present disclosure describes improved SELEX methods for producing aptamers that are capable of binding to target molecules and improved photoSELEX methods for producing photoreactive aptamers that are capable of both binding and covalently cross linking to target molecules. Specifically, the present disclosure describes methods for producing aptamers and photoaptamers having slower dissociation rate constants than are obtained using prior SELEX and photoSELEX methods. The disclosure further describes aptamers and photoaptamers having slower dissociation rate constants than those obtained using prior methods. In addition, the disclosure describes aptamer constructs that include a variety of functionalities, including a cleavable element, a detection element, and a capture or immobilization element.
PCT/US2008/070383 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rates WO2009012418A2 (en)

Priority Applications (12)

Application Number Priority Date Filing Date Title
MX2014005658A MX344253B (en) 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rates.
CN200880107336.0A CN101809167B (en) 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rates
EP08782010A EP2069529B1 (en) 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rates
EP17181688.7A EP3284832B1 (en) 2007-07-17 2008-07-17 Aptamer with improved rate of dissociation, and non-covalent aptamer-target complex thereof
MX2010000578A MX2010000578A (en) 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rates.
EP09012809.1A EP2172566B2 (en) 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rates
AU2008275915A AU2008275915B2 (en) 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rates
DK08782010.6T DK2069529T3 (en) 2007-07-17 2008-07-17 Process for generating aptamers with improved dissociation rates
JP2010517170A JP5684568B2 (en) 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rate
CA2696431A CA2696431C (en) 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rates
EP22162947.0A EP4056711A1 (en) 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rates
HK09111389.7A HK1133046A1 (en) 2007-07-17 2009-12-04 Method for generating aptamers with improved off-rates

Applications Claiming Priority (10)

Application Number Priority Date Filing Date Title
US95029307P 2007-07-17 2007-07-17
US95028307P 2007-07-17 2007-07-17
US95028107P 2007-07-17 2007-07-17
US60/950,283 2007-07-17
US60/950,293 2007-07-17
US60/950,281 2007-07-17
US3142008P 2008-02-26 2008-02-26
US61/031,420 2008-02-26
US5159408P 2008-05-08 2008-05-08
US61/051,594 2008-05-08

Publications (2)

Publication Number Publication Date
WO2009012418A2 WO2009012418A2 (en) 2009-01-22
WO2009012418A3 true WO2009012418A3 (en) 2009-03-05

Family

ID=40260081

Family Applications (3)

Application Number Title Priority Date Filing Date
PCT/US2008/070383 WO2009012418A2 (en) 2007-07-17 2008-07-17 Method for generating aptamers with improved off-rates
PCT/US2008/070371 WO2009012410A1 (en) 2007-07-17 2008-07-17 Improved selex and photoselex
PCT/US2008/070386 WO2009012420A1 (en) 2007-07-17 2008-07-17 Multiplexed analyses of test samples

Family Applications After (2)

Application Number Title Priority Date Filing Date
PCT/US2008/070371 WO2009012410A1 (en) 2007-07-17 2008-07-17 Improved selex and photoselex
PCT/US2008/070386 WO2009012420A1 (en) 2007-07-17 2008-07-17 Multiplexed analyses of test samples

Country Status (18)

Country Link
US (1) US8409795B2 (en)
EP (10) EP3284832B1 (en)
JP (11) JP5684568B2 (en)
KR (3) KR101634608B1 (en)
CN (5) CN107090457A (en)
AU (3) AU2008276001A1 (en)
CA (4) CA3022666C (en)
DK (4) DK3284832T3 (en)
ES (5) ES2647587T3 (en)
FI (1) FI3284832T3 (en)
HK (6) HK1133046A1 (en)
HR (1) HRP20150382T1 (en)
MX (6) MX2010000578A (en)
NO (1) NO2933340T3 (en)
PL (1) PL2489743T3 (en)
PT (2) PT2489743E (en)
SI (1) SI2489743T1 (en)
WO (3) WO2009012418A2 (en)

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